Election workers count votes at a polling station in Kabul after the disputed Afghan presidential election in August. Photograph: Simon Lim/AFP/Getty Images

Afghan election officials have begun logistical preparations for a second round of voting to determine the controversial presidential election marred by allegations of large-scale rigging in favour of Hamid Karzai, it emerged today.

The second round will take place in five weeks only if Karzai's share of the vote – which currently stands at 54% – falls to less than 50%. With 10% of ballots currently under scrutiny, that scenario appears increasingly likely.

Karzai's team today dismissed EU claims of fraud, after Phillippe Morillon, head of the EU election monitoring mission, said 1.1m of about 3m votes cast for Karzai were suspect.

"Hamid Karzai's election campaign team believes today's announcement of the number of suspected votes by the head and deputy head of EU election monitoring commission is partial, irresponsible and in contradiction with Afghanistan's constitution," his campaign office said in a statement.

A senior western official said that the Afghan independent election commission had "pencilled in" a run-off vote for the third week of October, despite earlier predictions that a fresh poll would be impossible before the onset of the harsh Afghan winter. The IEC has ordered new ballots from the UK and new stocks of indelible ink, used to stain voters' fingers, from Canada, according to the official, speaking on condition of anonymity. But an exact date has not been set.

A second vote could resolve a tense dispute with Karzai's main presidential rival, Abdullah Abdullah, who claims the 20 August poll was rigged. Results so far give Abdullah 28% support. But it would also be expensive and dangerous, disinfranchising Afghan voters in remote snowbound provinces. By the third week of October parts of northern Badakhshan and eastern Nuristan provinces are likely to be inaccessible because of heavy snowfall.

There would be a risk of further Taliban violence. In the last round, a small number of voters had their fingers chopped off after casting their ballot. The authorities would also have to recruit new staff in areas with a history of proven vote-rigging.

"It could be a nightmare. On top of the security problem of further Taliban attacks, some areas will be left out of the vote," the western official said.

So far, 93% of votes have been counted. The independent election commission is expected to release a full preliminary tally later today,, but the UN-backed electoral complaints commission (ECC), which adjudicates disputes, has quarantined votes from 2,500 of the country's 26,300 polling stations.

The ECC has already thrown out votes from 83 stations, mostly in areas in which Karzai won, in some cases scoring 100% of votes cast with a 100% turnout.

Despite the potential difficulties, many see an imperfect second round as preferable to a long winter of perilous limbo.

Alternatively, a second round could be averted if Karzai and Abdullah were to strike a power-sharing deal, but neither so far appears inclined to compromise.

The fraud controversy has split the UN mission to Kabul, whose American deputy head, Peter Galbraith, has left for New York following a dispute with his Norwegian boss, Kai Eide.

"In any hotly-contested election, there are bound to be differences of opinion. But Peter and Kai remain committed to the election process," a spokesman for the mission, Aleem Siddiqui, said.

The row is thought to centre on the UN's public stance on fraud allegations, with Galbraith favouring aggressive criticism while Eide advocates a "behind the scenes" approach.

One UN insider said the argument had divided opinion inside the mission, reflecting a wider split over the poll. "There's a heated debate in lots of embassies," the insider said. "The difference is that ours has come into the open."

The debates in Kabul came as the Ministry of Defence announced that two British soldiers had died yesterday after they were fatally wounded in separate explosions in southern Afghanistan.

A soldier from 2nd Battalion The Rifles was killed when he was caught in a blast while on foot patrol in Helmand and a second soldier, from 2nd Royal Tank Regiment, died in hospital in the UK after being injured in an explosion in the north-west of Helmand on Saturday. A total of 216 British troops have died in Afghanistan since the start of operations in October 2001.